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When comparing the spacecraft to other vehicles, just use the "everything else" value, ignore the propellant mass. This is because few earthly vehicles have total masses dominated by fuel mass as much as rockets are. How does 396.3 tons stack up?
Note: according to the blueprints the Michael Battleship (49) is 408 feet tall. However, this would make the Shuttle Orbiters mounted on the battleship too small. I scaled the blueprint so the Orbiters were at their official length, which made the Michael 433 feet tall.
Estimate somehow the volume (m 3 ) of your spacecraft. Calculate the mass by multiplying the volume by the average density (kg/m 3 ) of a spacecraft.